On Wed, Jun 20, 2012, Sanjib Paul wrote:
> I am simulating HCAII using 2CBA.pdb. I am using
> CaDA approach. I have changed residue name as given in the paper
> "Novel Zinc Protein Molecular Dynamics Simulation: Steps Toward
> Antiangiogenesis for Cancer Treatment, Yuan-Ping Pang, J. Mol. Model.
> 1999,5,196-202," After minimisation I have heated up the system using
> following input file,
> heating of whole system
> &cntrl
> imin = 0,
> irest = 0,
> iwrap = 1,
> ntx = 1,
> ntb = 1,
> ntc = 2,
> ntf = 2,
> ntt = 3,
> ntr = 1,
> cut = 20.0,
> tempi = 0.0,
> temp0 = 300.0,
> gamma_ln = 1.0,
> nstlim = 25000,
> dt = 0.002,
> ntpr = 100,
> ntwx = 100,
> ntwr = 1000
> /
> Keep protein fixed with weak restraint
> 3.0
> RES 1 265
> END
> END
>
> But, I am getting a follwing error, and run stopped after a time.
>
> vlimit exceeded for step 3680; vmax = 290.4790
> vlimit exceeded for step 3681; vmax = 5167.6693
>
> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 0 2017 4081 4082
>
> Note: This is usually a symptom of some deeper
> problem with the energetics of the system.
You need to stop the system shortly before step 3680 and examine what might be
odd. Certainly, use the default values for cut (i.e. 8.0) and dt (i.e.
0.001). That may enable you to get past the problem point. You could also
try heating first to 100K, then later to 300K. Also, the problem occurs
around atoms 4081 and 4082, so look especially there for odd behavior.
As the message states, there is generally some problem with the system or the
force field you are using (you don't say how you are handling the zinc atom),
so you probably have to do the trouble shooting: people on the list won't know
enough about your particular system to be of much help.
....dac
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Received on Wed Jun 20 2012 - 05:30:03 PDT
